Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

MK5 Proteome Analysis - Divided Values

Type II network, divided values. Interestingly most of the proteins in the first 100 positions in this table would occur in the divided ranks table between position 100 and 200, indicating a difference in emphasis between the two simulations but not in the overall function. The fully annotated table, include Ensembl gene identifiers and network values can be found in the supplementary data.


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Value Type Rank Gene description Interaction Map Network Comparison Type red Filtered green network_comparison
Results: HTML CSV LaTeX Showing element 1 to 50 of 77072 in total 
Value Type	Measured

Rank	description	Interaction Map	Network Comparison Type	red	Filtered	green	network_comparison	
1	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	High confidence	Subtracted	85	0	6410	6325	
1	ba508n22.1 (hspc025) (fragment). [source:sptrembl;acc:q9hcw5]	Low confidence	Subtracted	85	0	6410	6325	
1	carboxypeptidase d precursor (ec 3.4.17.-) (gp180). [source:swissprot;acc:o75976]	Low confidence	Subtracted	40899	1	32028.5	8870.5	
1	lysosome-associated membrane glycoprotein 1 precursor (lamp-1) (cd107a antigen). [source:swissprot;acc:p11279]	Low confidence	Divided	2399.5	1	543.5	4.4149	
1	mannosyl-oligosaccharide 1,2-alpha-mannosidase ib (ec 3.2.1.113) (processing alpha-1,2-mannosidase ib) (alpha-1,2-mannosidase ib) (mannosidase alpha class 1a member 2). [source:swissprot;acc:o60476]	High confidence	Subtracted	41482.5	1	33356.5	8126	
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	High confidence	Divided	364	0	0.00001	36400000	
1	mitochondrial 28s ribosomal protein s32 (s32mt) (mrp-s32) (ptd007) (hspc204). [source:swissprot;acc:q9y6g3]	Low confidence	Divided	364	0	0.00001	36400000	
1	rad50-interacting protein 1. [source:refseq;acc:nm_021930]	High confidence	Divided	450.5	1	2394.5	5.31521	
2	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	Low confidence	Subtracted	21185	1	28492	7307	
2	cab2. [source:refseq;acc:nm_033419]	High confidence	Divided	0.00001	0	174	17400000	
2	cell division protein kinase 4 (ec 2.7.1.37) (cyclin-dependent kinase 4) (psk-j3). [source:swissprot;acc:p11802]	Low confidence	Divided	2399.5	1	543.5	4.4149	
2	cytohesin 1 (sec7 homolog b2-1). [source:swissprot;acc:q15438]	High confidence	Subtracted	41482.5	1	33356.5	8126	
2	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	Low confidence	Divided	0.00001	0	89	8900000	
2	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	High confidence	Subtracted	85	0	6410	6325	
2	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Low confidence	Subtracted	23818.1	0	19621.3	4196.8	
2	rho-related btb domain-containing protein 2 (deleted in breast cancer 2 gene protein) (p83). [source:swissprot;acc:q9byz6]	High confidence	Divided	450.5	1	2394.5	5.31521	
3	cell division protein kinase 6 (ec 2.7.1.37) (serine/threonine protein kinase plstire). [source:swissprot;acc:q00534]	Low confidence	Divided	2399.5	1	543.5	4.4149	
3	cytohesin 2 (arf nucleotide-binding site opener) (arno protein) (arf exchange factor). [source:swissprot;acc:q99418]	High confidence	Subtracted	41482.5	1	33356.5	8126	
3	homeobox protein hlx1 (homeobox protein hb24). [source:swissprot;acc:q14774]	High confidence	Divided	2597.5	1	698.5	3.71868	
3	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	Low confidence	Divided	0.00001	0	89	8900000	
3	mitochondrial solute carrier protein. [source:refseq;acc:nm_145305]	Low confidence	Subtracted	21185	1	28492	7307	
3	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	High confidence	Subtracted	23818.1	0	19621.3	4196.8	
3	nucleoporin nup43 (p42). [source:swissprot;acc:q8nfh3]	Low confidence	Subtracted	5106.93	0	7500.75	2393.82	
3	pyridoxine 5'-phosphate oxidase. [source:refseq;acc:nm_018129]	High confidence	Divided	0.00001	0	109	10900000	
4	anchor attachment protein 1; glycophosphatidylinositol anchor attachment 1; anchor attachment protein 1 (gaa1p, yeast) homolog. [source:refseq;acc:nm_003801]	Low confidence	Subtracted	2082	0	4356	2274	
4	bestrophin (vitelliform macular dystrophy protein) (tu15b). [source:swissprot;acc:o76090]	Low confidence	Subtracted	36474.3	1	43509.4	7035.1	
4	cytohesin 4. [source:swissprot;acc:q9uia0]	High confidence	Subtracted	41482.5	1	33356.5	8126	
4	hbs1-like. [source:refseq;acc:nm_006620]	High confidence	Divided	2597.5	1	698.5	3.71868	
4	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	Low confidence	Divided	0.00001	0	89	8900000	
4	homeobox protein hox-c4 (hox-3e) (cp19). [source:swissprot;acc:p09017]	High confidence	Divided	0.00001	0	89	8900000	
4	lysosome-associated membrane glycoprotein 2 precursor (lamp-2) (cd107b antigen). [source:swissprot;acc:p13473]	Low confidence	Divided	2399.5	1	543.5	4.4149	
4	small nuclear ribonucleoprotein e (snrnp-e) (sm protein e) (sm-e) (sme). [source:swissprot;acc:p08578]	High confidence	Subtracted	18704	0	21730	3026	
5	cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [source:swissprot;acc:o43739]	High confidence	Subtracted	41482.5	1	33356.5	8126	
5	histone h4. [source:swissprot;acc:p02304]	High confidence	Subtracted	21773.1	0	24446.3	2673.2	
5	homeobox protein hox-c6 (hox-3c) (hho.c8) (cp25). [source:swissprot;acc:p09630]	High confidence	Divided	0.00001	0	89	8900000	
5	jumonji protein. [source:swissprot;acc:q92833]	Low confidence	Divided	0.00001	0	17.5166	1751660	
5	junctophilin 3 (junctophilin type 3) (jp-3). [source:swissprot;acc:q8wxh2]	High confidence	Divided	1153.5	1	339.5	3.39764	
5	lipopolysaccharide-responsive and beige-like anchor protein (cdc4-like protein) (beige-like protein). [source:swissprot;acc:p50851]	Low confidence	Subtracted	485.286	0	2740.13	2254.84	
5	oxysterol binding protein-related protein 6 (osbp-related protein 6) (orp-6). [source:swissprot;acc:q9bzf3]	Low confidence	Divided	736.5	1	2113.5	2.86965	
5	vitelliform macular dystrophy 2-like protein 2. [source:refseq;acc:nm_153274]	Low confidence	Subtracted	36469.3	1	43503.3	7034	
6	homeobox protein hox-a4 (hox-1d) (hox-1.4). [source:swissprot;acc:q00056]	High confidence	Divided	0.00001	0	89	8900000	
6	homogentisate 1,2-dioxygenase (ec 1.13.11.5) (homogentisicase) (homogentisate oxygenase) (homogentisic acid oxidase). [source:swissprot;acc:q93099]	Low confidence	Divided	13	0	0.00001	1300000	
6	junctophilin 2 (junctophilin type 2) (jp-2). [source:swissprot;acc:q9br39]	High confidence	Divided	1153.5	1	339.5	3.39764	
6	nuclear dna-binding protein; small unique nuclear receptor corepressor; c1d dna-binding protein. [source:refseq;acc:nm_006333]	Low confidence	Subtracted	36360.3	1	43368.8	7008.5	
6	oxysterol binding protein-related protein 3 (osbp-related protein 3) (orp-3). [source:swissprot;acc:q9h4l5]	Low confidence	Divided	736.5	1	2113.5	2.86965	
6	putative glialblastoma cell differentiation-related; putative glialblastoma cell differentiation-related protein. [source:refseq;acc:nm_016172]	High confidence	Subtracted	44490.5	1	36927.5	7563	
6	similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	High confidence	Subtracted	13174.7	0	15605.1	2430.4	
6	similar to zinc finger protein 277. [source:sptrembl;acc:q8wwa6]	Low confidence	Subtracted	7592.37	0	8836.85	1244.48	
7	28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [source:swissprot;acc:q9y2r5]	High confidence	Subtracted	21185	1	28492	7307	
7	cysteine endopeptidase aut-like 2 isoform a; autophagy-related cysteine endopeptidase 2; autophagin 2. [source:refseq;acc:nm_052936]	Low confidence	Subtracted	4660.09	0	5898.71	1238.62	

Legend:
- Rank is the rank after comparing the two networks
- Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
- Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
- Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
- Filtered specifies whether we only included the high confidence microarry measurements or not.
- http://analysis.yellowcouch.org/